SMED30033920

Overview
NameSMED30033920
Smed IDSMED30033920
Length (bp)320
Neoblast Clusters

Zeng et. al., 2018



 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30033920

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30033920h1SMcG0015474 SmedASXL_056014SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30033920h1SMcG0015473 dd_Smed_v4_10051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30033920h1SMcG0015474 dd_Smed_v4_10051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30033920h1SMcG0015474 dd_Smed_v6_62605_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
tail regionSMED30033920h1SMcG0015473 dd_Smed_v6_10051_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
tail regionSMED30033920h1SMcG0015474 dd_Smed_v6_10051_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033920 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001460:7129..7448 +1564
v31.001460:15100..15419 -1528
Homology
[Close]
BLAST of SMED30033920 vs. Planmine SMEST
Match: SMESG000031048.1 (SMESG000031048.1)

HSP 1 Score: 207.223 bits (526), Expect = 3.770e-65
Identity = 102/106 (96.23%), Postives = 104/106 (98.11%), Query Frame = 1 
Query:    1 VGLYFAYRIFMELIILFTPETWKFVYLLNKHFAEINLDLKSAFRVVSGNLAQHSATELATAYRYLIFFYVNLLLFSFITAFIVGFLNSLIQSFLILRNYRLHFQKI 318
            VGLYFAYRIFMELIILFTPETWKF+YLLNKHFAEINLDLKS FRVVSGNL+QHSATELATAYRYLIFFYVNLLLFSFI AFIVGFLNSLIQSFLILRNYRLHFQKI
Sbjct:  252 VGLYFAYRIFMELIILFTPETWKFIYLLNKHFAEINLDLKSGFRVVSGNLSQHSATELATAYRYLIFFYVNLLLFSFIAAFIVGFLNSLIQSFLILRNYRLHFQKI 357
[Close]
BLAST of SMED30033920 vs. Planmine SMEST
Match: SMESG000041908.1 (SMESG000041908.1)

HSP 1 Score: 207.608 bits (527), Expect = 2.044e-63
Identity = 103/106 (97.17%), Postives = 105/106 (99.06%), Query Frame = 1 
Query:    1 VGLYFAYRIFMELIILFTPETWKFVYLLNKHFAEINLDLKSAFRVVSGNLAQHSATELATAYRYLIFFYVNLLLFSFITAFIVGFLNSLIQSFLILRNYRLHFQKI 318
            VGLYFAYRIFMELIILFTPETWKF+YLLNKHFAEINLDLKSAFRVVSGNL+QHSATELATAYRYLIFFYVNLLLFSFI AFIVGFLNSLIQSFLILRNYRLHFQKI
Sbjct: 1070 VGLYFAYRIFMELIILFTPETWKFIYLLNKHFAEINLDLKSAFRVVSGNLSQHSATELATAYRYLIFFYVNLLLFSFIAAFIVGFLNSLIQSFLILRNYRLHFQKI 1175

HSP 2 Score: 139.043 bits (349), Expect = 2.429e-39
Identity = 68/107 (63.55%), Postives = 84/107 (78.50%), Query Frame = 1 
Query:    1 VGLYFAYRIFMELIILFTPETWKFVYLLNKHFAEINL-DLKSAFRVVSGNLAQHSATELATAYRYLIFFYVNLLLFSFITAFIVGFLNSLIQSFLILRNYRLHFQKI 318
            VGLYFAYRIFM+ II  TP+ W  +YL+NK F+  N  ++KSAF++VSGN +Q+S  ++  A+RYL FFY NLLL   I A I+GFLNSLIQSFLILRN+RLHFQKI
Sbjct:  159 VGLYFAYRIFMDQIIALTPQGWDIIYLINKKFSTTNTTNIKSAFQIVSGNYSQYSEIKIINAFRYLAFFYTNLLLGCLIAAIIIGFLNSLIQSFLILRNFRLHFQKI 265
[Close]
BLAST of SMED30033920 vs. Planmine SMEST
Match: SMESG000031041.1 (SMESG000031041.1)

HSP 1 Score: 139.813 bits (351), Expect = 7.703e-40
Identity = 66/106 (62.26%), Postives = 82/106 (77.36%), Query Frame = 1 
Query:    1 VGLYFAYRIFMELIILFTPETWKFVYLLNKHFAEINLDLKSAFRVVSGNLAQHSATELATAYRYLIFFYVNLLLFSFITAFIVGFLNSLIQSFLILRNYRLHFQKI 318
            VGLYFAYRIFM+ II  TP+ W  +YL+N+ F   + ++KSAF +VSGN +Q+S  ++  A+RYL FFY NLLL   I A I+GFLNSLIQSFLILRN+RLHFQKI
Sbjct:  286 VGLYFAYRIFMDQIIALTPQGWDIIYLINQRFYTTDTNMKSAFEIVSGNYSQYSEIKIINAFRYLTFFYTNLLLGCLIAAIIIGFLNSLIQSFLILRNFRLHFQKI 391
[Close]
BLAST of SMED30033920 vs. Planmine SMEST
Match: SMESG000031046.1 (SMESG000031046.1)

HSP 1 Score: 128.642 bits (322), Expect = 6.423e-36
Identity = 61/106 (57.55%), Postives = 79/106 (74.53%), Query Frame = 1 
Query:    1 VGLYFAYRIFMELIILFTPETWKFVYLLNKHFAEINLDLKSAFRVVSGNLAQHSATELATAYRYLIFFYVNLLLFSFITAFIVGFLNSLIQSFLILRNYRLHFQKI 318
            VGLYFAYRIFM+ II  TP+ W  +YL+NK  +  N+++KSAF +VSGN +++S  ++  A+ YL  FY NL L   I   ++GFLNSLIQSFLILRN+RLHFQKI
Sbjct:  293 VGLYFAYRIFMDQIIDLTPQGWTVIYLINKGISNTNINMKSAFLIVSGNYSKYSEVKIINAFSYLTLFYTNLFLGCLIFGTVIGFLNSLIQSFLILRNFRLHFQKI 398
[Close]
BLAST of SMED30033920 vs. Planmine SMEST
Match: SMESG000031061.1 (SMESG000031061.1)

HSP 1 Score: 90.8929 bits (224), Expect = 1.273e-22
Identity = 44/106 (41.51%), Postives = 69/106 (65.09%), Query Frame = 1 
Query:    1 VGLYFAYRIFMELIILFTPETWKFVYLLNKHFAEINLDLKSAFRVVSGNLAQHSATELATAYRYLIFFYVNLLLFSFITAFIVGFLNSLIQSFLILRNYRLHFQKI 318
            VGLYFAYRIF++ I+  TP  WK +  +N  +     ++  +F ++  N + +S  E+  ++RYL F Y +LL+   ++A  + F+NS+IQS L+LRNYRLHF +I
Sbjct:  170 VGLYFAYRIFIDNILGLTPIAWKLIAEINNKYLITQTNISRSFYLIWSNYSLYSKMEIQNSFRYLTFSYTHLLISCLLSAIFIAFINSVIQSLLLLRNYRLHFHRI 275
The following BLAST results are available for this feature:
BLAST of SMED30033920 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033920 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000031048.13.770e-6596.23SMESG000031048.1[more]
SMESG000041908.12.044e-6397.17SMESG000041908.1[more]
SMESG000031041.17.703e-4062.26SMESG000031041.1[more]
SMESG000031046.16.423e-3657.55SMESG000031046.1[more]
SMESG000031061.11.273e-2241.51SMESG000031061.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033920 ID=SMED30033920|Name=SMED30033920|organism=Schmidtea mediterranea sexual|type=transcript|length=320bp
GTTGGATTGTATTTTGCTTATCGGATTTTCATGGAGCTAATCATTTTATT
TACGCCAGAAACCTGGAAATTCGTTTATTTGTTGAATAAACATTTTGCTG
AAATTAATTTAGATTTGAAGTCTGCTTTTCGAGTCGTCTCAGGAAATCTT
GCTCAACATTCCGCTACTGAATTGGCAACCGCCTACAGATATTTAATATT
TTTTTACGTAAACCTTCTGCTCTTTAGTTTCATTACTGCCTTTATTGTGG
GATTTTTAAACTCCTTGATTCAATCGTTCTTGATTTTGAGAAATTATCGG
CTACATTTTCAGAAAATCAG
back to top

protein sequence of SMED30033920-orf-1

>SMED30033920-orf-1 ID=SMED30033920-orf-1|Name=SMED30033920-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
VGLYFAYRIFMELIILFTPETWKFVYLLNKHFAEINLDLKSAFRVVSGNL
AQHSATELATAYRYLIFFYVNLLLFSFITAFIVGFLNSLIQSFLILRNYR
LHFQKI
back to top
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 64..86